After requests I added yesterday more visible the RSS and Atom feeds for the Planet Blue Obelisk. They are linked in the menu on the right, and as alternative links to the document. These should show up in most recent webbrowsers as feed icon in the lower right corner of the browser window. It is often an orange icon. I also added a ‘Leave a comment’ link to encourage people to leave comments on items.
Stefan has done an excellent debugging week on JChemPaint, while I have been late with a 2.1 release. Anyway, I’ve just uploaded a Java 1.4 compiled JChemPaint 2.1 series release. I was told the (reported) bug count is down to one, so I expect to see the next stable branch to be released soon (2.2 series). But what after JChemPaint 2.2 gets released? Will a 2.3 developers branch be opened?
KDE 3.5 was released with lots of changes. SuperKaramba is now a standard KDE application and is neatly integrated. It allows embedding themelets on your desktop background. It shows several themelets: the weather, a calender, a toolbar with applications, a FoldingAtHome monitor , the contents of the clipboard, the music that is playing (Cake) and a simple todo list. All customizable up to the pixel.
Getting Started with Eclipse and the SWT is a very nice set of introductory tutorial on working with SWT and Eclipse in general. The tutorials cover the basic, advanced SWT widgets, SWT layout, and several other interesting topics. Now that Bioclipse is gaining speed, it is a must-read.
Today I setup a blog planet for Blue Obelisk members. First I tried Chumpologica but it did not read Atom feeds. Next in line was Planet , which turned out to be used by many big planet sites, like Planet Debian . It also works with Atom feeds in general, but not well with Atom 1.0 feeds, like that of Carsten. After some googling I found a patched version which did the job.
Where I was able to mention earlier that JChemPaint now runs with free (as in open source) Java virtual machines, I just tried to run the core Jmol renderer, using the Integration.java which comes as an example. Sadly, the original screenshots got lost there were made with jamvm 1.3.3 and classpath 0.19. It is very slow, however. I have not tried it with other free virtual machines, which are supposedly faster.
Doesn’t happen often, but my machine crashed two hours ago. Not a big deal, because I have my important files in SVN. Oh wait, SVN had a commit in progress during the crash. So, svn recover. Mmmm… doesn’t work either. OK, SVN FAQ: try db_recover. That worked. No, it did not: svn commit still not working for the files I was trying to commit.
Some weeks back there was the CDK5AW , the CDK 5th anniversiry workshop. A small group of international open source chemo-, bioinformatics software developers met, among which two from Sweden. It was then decided to generalize their work resulting in Bioclipse: https://www.bioclipse.net/ It’s heavily using the Eclipse Rich Client Platform , making additional plugins trivial.
Thanx to Mark’s encouragements, I tried to run Jmol and JChemPaint with jamvm. Jmol fails with an NullPointerException , but JChemPaint runs! And note that this was not even running with the latest of the latest; just recent packages from Kubuntu! Yes, there are some glitches, but I’m happy nevertheless!
This evening I have been looking at with the KNOPPIX customization howto, and ran many of the interesting commands. I’ve setup a environment with Kalzium, OpenBabel, CDK, jython, PyMOL, and for development I included gcj and Eclipse. At some later point I will include kfile_chemical too, but I want to make a deb package first.